Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Transcriptomics
slides
Reference-based RNA-Seq data analysis
tutorial zenodo_link workflow interactive_tour
De novo transcriptome reconstruction with RNA-Seq
tutorial zenodo_link workflow interactive_tour

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
1: RNA-Seq reads to counts
tutorial zenodo_link workflow
2: RNA-seq counts to genes
tutorial zenodo_link workflow
3: RNA-seq genes to pathways
tutorial zenodo_link workflow

Single-cell RNA-seq

Tutorials about analysis of single-cell RNA-seq data

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
An introduction to scRNA-seq data analysis
slides / video
Pre-processing of Single-Cell RNA Data
slides tutorial zenodo_link workflow
Understanding Barcodes
tutorial zenodo_link
Plates, Batches, and Barcodes
slides / video
Single-cell quality control with scater
tutorial zenodo_link workflow
Downstream Single-cell RNA analysis with RaceID
tutorial zenodo_link workflow
Pre-processing of 10X Single-Cell RNA Datasets
tutorial zenodo_link workflow
Clustering 3K PBMCs with Scanpy
slides tutorial zenodo_link workflow
Analysis of plant scRNA-Seq Data with Scanpy
tutorial zenodo_link workflow

Single-cell RNA-seq: Case Study

Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Generating a single cell matrix using Alevin
tutorial zenodo_link workflow
Filter, Plot and Explore Single-cell RNA-seq Data
tutorial zenodo_link workflow
Trajectory Analysis using Python (Jupyter Notebook) in Galaxy
tutorial zenodo_link

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
RNA Seq Counts to Viz in R
tutorial zenodo_link
Visualization of RNA-Seq results with CummeRbund
slides tutorial zenodo_link interactive_tour
Visualization of RNA-Seq results with heatmap2
tutorial zenodo_link workflow
Visualization of RNA-Seq results with Volcano Plot
level level level
tutorial zenodo_link workflow
Visualization of RNA-Seq results with Volcano Plot in R
level level level
tutorial zenodo_link

Other


Assorted other tutorials

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
CLIP-Seq data analysis from pre-processing to motif detection
tutorial zenodo_link workflow interactive_tour
Differential abundance testing of small RNAs
tutorial zenodo_link workflow interactive_tour
GO Enrichment Analysis
tutorial zenodo_link workflow
Network analysis with Heinz
slides tutorial zenodo_link workflow interactive_tour
RNA-RNA interactome data analysis
tutorial zenodo_link workflow
RNA-Seq analysis with AskOmics Interactive Tool
slides tutorial zenodo_link
Small Non-coding RNA Clustering using BlockClust
tutorial zenodo_link workflow
Whole transcriptome analysis of Arabidopsis thaliana
slides / video tutorial zenodo_link workflow

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

Bérénice BatutBérénice Batut Maria DoyleMaria Doyle Florian HeylFlorian Heyl

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Maria DoyleMaria Doyle Belinda PhipsonBelinda Phipson Harriet DashnowHarriet Dashnow Jovana MaksimovicJovana Maksimovic Anna TrigosAnna Trigos Matt RitchieMatt Ritchie Shian SuShian Su Charity LawCharity Law Florian HeylFlorian Heyl Daniel MaticzkaDaniel Maticzka Bérénice BatutBérénice Batut Mallory FreebergMallory Freeberg IGC Bioinformatics UnitIGC Bioinformatics Unit Chao (Cico) ZhangChao (Cico) Zhang Fotis E. PsomopoulosFotis E. Psomopoulos Toby HodgesToby Hodges Pavankumar VidemPavankumar Videm Xavier GarnierXavier Garnier Anthony BretaudeauAnthony Bretaudeau Anne SiegelAnne Siegel Olivier DameronOlivier Dameron Mateo BoudetMateo Boudet Andrea BagnacaniAndrea Bagnacani Cristóbal GallardoCristóbal Gallardo Beatriz Serrano-SolanoBeatriz Serrano-Solano Anika ErxlebenAnika Erxleben Markus WolfienMarkus Wolfien Mehmet TekmanMehmet Tekman Wendi BaconWendi Bacon Jonathan ManningJonathan Manning Wolfgang MaierWolfgang Maier Mo HeydarianMo Heydarian Clemens BlankClemens Blank Nicola SoranzoNicola Soranzo Peter van HeusdenPeter van Heusden Alex OstrovskyAlex Ostrovsky Graham EtheringtonGraham Etherington Hans-Rudolf HotzHans-Rudolf Hotz Daniel BlankenbergDaniel Blankenberg

References